Table 9.
Position, SNP alleles, estimated effects of SNPs for marbling score (1–9) that were detected at 5% chromosome-wise level
| SNP1) | Chr | Position (bp)2) | Allele3) | MAF | Estimates of SNPs effects4) | Significance (−log10P5)) | Nearest gene6) | ||
|---|---|---|---|---|---|---|---|---|---|
|
|
|
||||||||
| Additive | Dominance | Name | Distance (bp) | ||||||
| BTB-00126406 | 3 | 35,420,885 | T/C | T(0.08) | 2.04±0.41 | −1.55±0.44 | 5.78 | KCNA3 | 6,892 |
| Hapmap39048-BTA-99764 | 3 | 44,502,770 | T/G | T(0.30) | 0.53±0.12 | - | 4.81 | EDG1 | within |
| BTB-00137937 | 3 | 87,445,557 | G/A | A(0.15) | - | 0.91±0.18 | 6.32* | ROR1 | within |
| Hapmap3063-BTA-15439 | 5 | 109,235,854 | C/A | C(0.16) | - | −0.72±0.17 | 4.57 | LOC751811 | 2,138 |
| UA-IFASA-5392 | 7 | 61,523,523 | T/C | C(0.17) | −0.68±0.16 | - | 4.89 | LOC100138980 | 11,789 |
| BTB-00317097 | 7 | 65,652,720 | T/C | C(0.25) | −0.59±0.13 | - | 4.88 | LOC784642 | 39,676 |
| BFGL-NGS-114649 | 7 | 69,609,512 | T/G | T(0.37) | −0.36±0.13 | −0.32±0.16 | 3.91 | EPN4 | 409,625 |
| ARS-BFGL-NGS-63249 | 7 | 71,629,520 | T/C | C(0.47) | 0.36±0.11 | 0.49±0.15 | 4.06 | FABP6 | 6,896 |
| Hapmap40812-BTA-80049 | 7 | 80,713,755 | T/C | T(0.11) | 1.39±0.35 | −0.90±0.38 | 3.97 | ODZ2 | within |
| Hapmap25504-BTA-125586 | 10 | 53,007,997 | G/A | G(0.24) | 0.90±0.18 | −0.77±0.21 | 5.17 | GRINL1A | 113,126 |
| ARS-BFGL-NGS-73404 | 13 | 54,520,958 | T/C | C(0.10) | 0.84±0.20 | * | 4.73 | PRPF6 | within |
| BTB-00633720 | 16 | 27,646,807 | T/G | T(0.12) | 0.73±0.18 | - | 4.06 | EPB41L3 | within |
| Hapmap26379-BTA-130999 | 16 | 51,370,098 | T/C | T(0.37) | 0.50±0.12 | - | 4.71 | PDPN | 12,031 |
| Hapmap60996-rs29015760 | 17 | 25,742,715 | C/A | C(0.15) | - | 0.75±0.18 | 4.45 | LOC539187 | 72,892 |
| BTB-00689316 | 17 | 73,276,535 | T/C | C(0.43) | - | −0.62±0.15 | 4.26 | MORC2 | within |
| ARS-BFGL-NGS-107813 | 18 | 33,279,345 | C/A | A(0.32) | - | −0.64±0.15 | 4.60 | TK2 | within |
| ARS-BFGL-NGS-55014 | 18 | 39,198,464 | G/A | A(0.49) | 0.31±0.11 | −0.53±0.15 | 4.37 | HYDIN | within |
| Hapmap40994-BTA-46361 | 19 | 62,959,153 | T/C | T(0.35) | 0.50±0.12 | - | 4.18 | MAP2K6 | 78,574 |
| ARS-BFGL-NGS-36359 | 19 | 63,936,266 | T/C | C(0.13) | −0.68±0.17 | - | 4.25 | RGS9 | 38,731 |
| ARS-BFGL-NGS-16187 | 25 | 8,839,364 | G/A | A(0.45) | −0.33±0.12 | −0.59±0.15 | 4.62 | LOC538487 | 37,048 |
| BTB-111681-no-rs | 26 | 10,857,884 | G/A | G(0.13) | - | −0.75±0.19 | 4.12 | LIPK | within |
| BTB-00978135 | 28 | 12,940,047 | T/G | T(0.37) | - | −0.61±0.15 | 4.15 | BICC1 | 21,033 |
SNP, single nucleotide polymorphism; MAF, minor allele frequency; QTL, quantitative trait loci.
1),2)
SNP marker annotations and their positions were based on the bovine reference genome (btau4.0).
3)
Nucleotides of substitution.
4)
Estimates of additive and dominance effects with standard errors.
5)
Negative logarithm of the comparison-wise p-value of the test-statistic against the null hypothesis of no QTL at the most likely position for the inferred QTL model.
6)
The nearest known gene to the significant SNP.
*
Significant at the 5% genome-wise level.